Metagenome/metatranscriptome db with blast option?

Question

[jahcubt]

Hello, I'm looking for metagenomic/metatranscriptomic databases online that you can blast a reference sequence against (besides NCBI). So far, the only useful one I have found that has allowed me to do this is IMG/JGI. I'm looking at the diversity of a family of endoparasitic organisms, so looking at data already available first.

Is there a scarcity, or am I just not looking properly?

Thanks for any help in advance, JT.

[arnstrm]

Just want to make sure, you are not referring to 16srRNA data as metagenomic/metatranscriptomic data, right?. Can't you just use the regular NCBI NR database to classify your sequences? If you have large number of sequences, I wouldn't use the online GUI interface to blast and I would just run it locally on command line. If you are using only 16s sequences, then you can either subset the ncbi database or use multiple 16srRNA databases (greengenes, silvia, RDB) to blast against. Let me need more instructions, I'll post a detailed answer!

[jahcubt]

No, I'm referring to 18srRNA (probably should have mentioned that. So a fair few databases aren't of much help, as they do seem to be mainly 16s based.

I may not have explained myself well. So I'm not trying to classify my sequences, I'm trying to find sequences similar to the sequence of known species that I have. So I can have a better idea of the distributions/diversity of related species that are not available on NCBI.

Answer 1

[ALchEmiXt]

If you have full metagenomic data (so not only 16S-amplicon barcoding as mentioned above) you could give metaphlan2 a try. We have good experience with their taxa specific reference database. It has to be run locally though: https://bitbucket.org/biobakery/metaphlan2

[jahcubt]

This looks quite good, I'll give it a go. Thanks.